Population genomics in practice

What is population genomics?

Per Unneberg

NBIS

12/15/22

A brief history of population genetics

Mendel’s peas

Galton, Pearson and Bateson

Of blending and particulate inheritance (the latter championed by Bateson)

Morgan’s flies

Fisher and natural selection

The modern synthesis

Wright and drift

Kimura and the diffusion approximation

What is population genomics?

What is population genomics?

Points from (Hahn, 2019):

  • whole-genome data instead of single loci - population genomics is population genetics for whole-genome sequences
    • if only this, not too exciting
  • major promise: enables analyses not possible for single loci or that require genomic context
  • addresses interactions between different forces, notably selection and demographic history

Some applications:

  • genome-wide scans for selection
    • selection vs demography
  • methods for genome-wide scans
  • non-independence
    • different statistics rely on similar input
    • overlapping peaks from different statistics not independent

(Hartl & Clark, 1997, pp. 469–470)

An example from real life - population genetics of coral

Figure 1: Genome assembly and sampling

Figure 2: Variation and demographic history

Figure 3: Selection scan

Figure 4: Population structure

Fuller et al. (2020)

Statistical inference in population genomics

(Johri et al., 2022)

Population genomics in the future

List stuff we won’t have time to go through

Machine learning and AI for population genomics

Ancestral recombination graph methods

  • deep population sequencing - tskit was developed to handle data size

Ancient DNA

Coalescent and Wright-Fisher simulations

Use to determine significance in genome-wide scans

Population genomics in practice

Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N., Shepherd, J., Sarre, L., Peng, J., Liao, Y., Pickrell, J., Andolfatto, P., Matz, M., Bay, L. K., & Przeworski, M. (2020). Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 369(6501), eaba4674. https://doi.org/10.1126/science.aba4674
Hahn, M. (2019). Molecular Population Genetics (First). Oxford University Press.
Hartl, D. L., & Clark, A. G. (1997). Principles of population genetics. Sinauer Associates.
Johri, P., Aquadro, C. F., Beaumont, M., Charlesworth, B., Excoffier, L., Eyre-Walker, A., Keightley, P. D., Lynch, M., McVean, G., Payseur, B. A., Pfeifer, S. P., Stephan, W., & Jensen, J. D. (2022). Recommendations for improving statistical inference in population genomics. PLOS Biology, 20(5), e3001669. https://doi.org/10.1371/journal.pbio.3001669
Li, H., & Durbin, R. (2011). Inference of human population history from individual whole-genome sequences. Nature, 475(7357), 493–496. https://doi.org/10.1038/nature10231